ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CGGAATATGTGATTCCTCTCATCTTCCCATTACTCACAGCACATCAACTGAATGTACAACAATTTGCCAAGTATATGCTATTTGTCAAGGACATTACAAGgtattgtttatcctgcattgctctcctgtgtccattaatatgtcaactaaactactacctatttctacag

Basic information

species	Zea mays
transcript	GRMZM2G061681_T01
intron #	13
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G061681_T02 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os01g42950.2 (Oryza sativa), 5'ss of exon 13

CGGAATATGTGATTCCTCTCATCTTCCCATTACTCACAGCACATCAACTGAATGTACAACAATTTGCCAAGTATATGCTATTTGTCAAGGACATTACAAGgtattgtttatcctgcattgctctcc-tgtgtccattaatatgtcaactaaactactacctatttctacag----
|||| || |||||||||||| |||||||| | |||||||||||||||||||||||||| |||||||| ||||| || |||||||||||||| || ||||||||   ||| |||  |    ||  |  || ||  || |||||| |||||||| || | |||| ||||||||    
CGGAGTACGTGATTCCTCTCGTCTTCCCACTGCTCACAGCACATCAACTGAATGTACAGCAATTTGCTAAGTACATACTATTTGTCAAGGATATCACAAGgtaccttttgtcccaccacacttgcgatgcgttaatcaatatgccaactaaattagtgcctacttctacagcaag

upper sequence: GRMZM2G061681_T02 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os01g42950.1 (Oryza sativa), 5'ss of exon 13

CGGAATATGTGATTCCTCTCATCTTCCCATTACTCACAGCACATCAACTGAATGTACAACAATTTGCCAAGTATATGCTATTTGTCAAGGACATTACAAGgtattgtttatcctgcattgctctcc-tgtgtccattaatatgtcaactaaactactacctatttctacag
|||| || |||||||||||| |||||||| | |||||||||||||||||||||||||| |||||||| ||||| || |||||||||||||| || ||||||||   ||| |||  |    ||  |  || ||  || |||||| |||||||| || | |||| ||||||||
CGGAGTACGTGATTCCTCTCGTCTTCCCACTGCTCACAGCACATCAACTGAATGTACAGCAATTTGCTAAGTACATACTATTTGTCAAGGATATCACAAGgtaccttttgtcccaccacacttgcgatgcgttaatcaatatgccaactaaattagtgcctacttctacag

upper sequence: GRMZM2G061681_T02 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA12G37070.1 (Glycine max), 5'ss of exon 13

CGGAATATGTGATTCCTCTCATCTTCCCATTACTCACAGCACATCAACTGAATGTACAACAATTTGCCAAGTATATGCTATTTGTCAAGGACATTACAAGgtattgtttatcctgc--------attgctctcctgtgtccattaatat--gtcaactaaactactacctatttct-acag------------------------------------------
| ||  ||||  ||||  |  |  | ||  | || || || || ||| ||||||| ||||| |||||||| |||||||| ||||||||||| ||      ||| | |||    |          |||   | ||| | |   ||  |||  |||  |   | |       || ||| |||                                           
CTGAGCATGTTCTTCCATTGCTTATACCCCTGCTGACTGCTCAACAATTGAATGTTCAACAGTTTGCCAAATATATGCTCTTTGTCAAGGATATGCTCCAgtaatattttcttttttaaaaaaaattaagcccctctattttttgttatctgtcttcctcattgtccttaatctctgacaaacttctctttaattttttttttgaactttgtgctctgtacag

upper sequence: GRMZM2G061681_T02 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA09G00470.1 (Glycine max), 5'ss of exon 13

CGGAATATGTGATTCCTCTCATCTTCCCATTACTCACAGCACATCAACTGAATGTACAACAATTTGCCAAGTATATGCTATTTGTCAAGGACATTACAAGgtattgtttatcctgcattgctctcctgtgtccattaatatgtcaactaaactactacctatttctacag----------------------------------------------------------------
| ||  || |  ||||  |  |  | ||  | || || || |  ||| ||||||| ||||| |||||||| |||||||| ||||||||||| ||      ||| | ||| |  |  ||   |||  |    || | | | | |  | | |  | ||  || | ||                                                                     
CTGAGCATCTTCTTCCATTGCTTATGCCCCTGCTGACTGCTCCACAATTGAATGTTCAACAGTTTGCCAAATATATGCTCTTTGTCAAGGATATGCTCCAgtaat-ttttttttaaataattct--taaccccctcattttttttatttattttctgtctttctcattgtccttgatctctgacaaacttctcttttttttttttttttaaaaaaaaaactgtgttctgtatag

upper sequence: GRMZM2G061681_T02 (Zea mays), 5'ss of exon 13
lower sequence: AT1G71410.1 (Arabidopsis thaliana), 5'ss of exon 13

CGGAATATGTGATTCCTCTCATCTTCCCATTACTCACAGCACATCAACTGAATGTACAACAATTTGCCAAGTATATGCTATTTGTCAAGGACATTACAAGgtat-----tgtttatcctgcattgctctcctgt-gtccattaatatgtcaactaaactactacc--tatttctacag--------------------------
| ||| ||||| || | || ||  | ||  | ||||| || || |||||||| || ||||| |||||||| |||||||||||||||||||| |||   |||| |     |  |||||   || | || |    | ||   || |  |    || | |  | |     | | | ||  |                          
CAGAACATGTGCTTACCCTGATGATGCCGCTTCTCACTGCCCAACAACTGAACGTCCAACAGTTTGCCAAATATATGCTATTTGTCAAGGATATTCTCAGgtgtgcatcttgttatcagtcagtacttttgaatagtgttttcacgtccgtaccacaacagtgttgttgtctttattgtgatttgtattcatctattgtaacag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments

ATGC    EST sequence
ATGC    genomic sequence (exon)
ATGC    genomic sequence (truncated intron)

EST: gi|211454621|gb|FL182680.1|FL182680

EST:     AATGTACAACAATTTGCCAAGTATATGCTATTTGTCAAGGACATTACAAG                         CAAGATCGAAGAGAAGCGTGGTGTGACTGTTACAGATAATGGGAACACAGA
genomic: AATGTACAACAATTTGCCAAGTATATGCTATTTGTCAAGGACATTACAAGgtattgttta ... atttctacagCAAGATCGAAGAGAAGCGTGGTGTGACTGTTACAGATAATGGGAACACAGA

RNA-Seq data

ATGC Supported by RNA-Seq exonic block that spans over the splice site

atgs Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.

Found data for 4 RNA-Seq libraries.

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 208

CGGAATATGTGATTCCTCTCATCTTCCCATTACTCACAGCACATCAACTGAATGTACAACAATTTGCCAAGTATATGCTATTTGTCAAGGACATTACAAGgtattgttta ... atttctacagCAAGATCGAAGAGAAGCGTGGTGTGACTGTTACAGATAATGGGAACACAGAGGTAAAAGCATCACCTTCATTGGCAAACGGGATCCATTCTGAACCTATG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 281

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 268